Publications des doctorants SDSV

L'école doctorale SDSV

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Les publications sont classées en ordre alphabétique de premier auteur. Le nom des doctorants SDSV est en gras.
Seules figurent les publications acceptées ou publiées.


- Aghakhani S., Zerrouk N. and Niarakis A. (2020) Metabolic Reprogramming of Fibroblasts as Therapeutic Target in Rheumatoid Arthritis and Cancer: Deciphering Key Mechanisms Using Computational Systems Biology Approaches. 13(1), 35;

- Arnaiz O, Meyer E, Sperling L. (2020) ParameciumDB 2019: integrating genomic data across the genus for functional and evolutionary biology. Nucleic Acids Res, 48(D1):D599-D605. doi: 10.1093/nar/gkz948.

- Asif-Laidin A, Conesa C, Bonnet A, Grison C, Adhya I, Menouni R, Fayol H, Palmic N, Acker J, Lesage P (2020) A small targeting domain in Ty1 integrase is sufficient to direct retrotransposon integration upstream of tRNA genes. EMBO J, 39 (17) e104337. doi: 10.15252/embj.2019104337. Epub 2020 Jul 17.

- Aubry C, Clerici P, Gerbaud C, Micouin L, Pernodet JL, Lautru S. (2020) Revised Structure of Anthelvencin A and Characterization of the Anthelvencin Biosynthetic Gene Cluster. ACS Chem Biol doi: 10.1021/acschembio.9b00960. [Epub ahead of print]

- Badel C, Da Cunha V, Forterre P, Oberto J. (2020) Pervasive suicidal integrases in deep-sea archaea. Mol Biol Evol, pii: msaa041. doi: 10.1093/molbev/msaa041. [Epub ahead of print]

- Badel C, Da Cunha V, Catchpole R, Forterre P, Oberto J. (2020) WASPS: web-assisted symbolic plasmid synteny server. Bioinformatics, 36(5):1629-1631. doi: 10.1093/bioinformatics/btz745.

- Bastaraud A, Cecchi P, Handschumacher P, Altmann M, Jambou R. (2020) Urbanization and Waterborne Pathogen Emergence in Low-Income Countries: Where and How to Conduct Surveys? Int J Environ Res Public Health,17(2). pii: E480. doi: 10.3390/ije20480. Review.

- Bazin A, Gautreau G, Médigue C, Vallenet D, Calteau A. (2020) panRGP: a pangenome-based method to predict genomic islands. Bioinformatics, 36(Supplement_2):i651-i658. doi: 10.1093/bioinformatics/btaa792

- Belot L, Ouldali M, Roche S, Legrand P, Gaudin Y, Albertini AA. (2020) Crystal structure of Mokola virus glycoprotein in its post-fusion conformation. PLoS Pathog, 16(3):e1008383. doi: 10.1371/journal.ppat.1008383. eCollection 2020 Mar.

- Bodakuntla S, Schnitzler A, Villablanca C, Gonzalez-Billault C, Bieche I, Janke C, Magiera MM. (2020) Tubulin polyglutamylation is a general traffic-control mechanism in hippocampal neurons. J Cell Sci, 133(3). pii: jcs241802. doi: 10.1242/jcs.241802.

- Bodakuntla S, Magiera MM, Janke C. (2020) Measuring the Impact of Tubulin Posttranslational Modifications on Axonal Transport. Methods Mol Biol, 2101:353-370. doi: 10.1007/978-1-0716-0219-5_20.

- Bodakuntla S, Jijumon AS, Janke C, Magiera MM.Purification of Tubulin with Controlled Posttranslational Modifications and Isotypes from Limited Sources by Polymerization-Depolymerization Cycles. J Vis Exp. 2020 Nov 5;(165). doi: 10.3791/61826.

- Breban M, Beaufrère M, Glatigny S. (2020) The microbiome in spondyloarthritis. Best Pract Res Clin Rheumatol, 12:101495. doi: 10.1016/j.berh.2020.101495. [Epub ahead of print] Review.

- Bridel S, Bourgeon F, Marie A, Saulnier D, Pasek S, Nicolas P, Bernardet JF, Duchaud E. (2020) Genetic Diversity and Population Structure of Tenacibaculum maritimum, a Serious Bacterial Pathogen of Marine Fish: From Genome Comparisons to High Throughput MALDI-TOF Typing. Vet Res, 7;51(1):60. doi: 10.1186/s13567-020-00782-0.

- Charlier P, Froesch P, Prades L, Augias A, Perciaccante A, Appenzeller O, Lippi D, Balloni S, Bianucci R. (2020) Further anthropological and pathological arguments related to St Louis' scurvy and infection signs on the Notre-Dame mandible (Paris, France). J Stomatol Oral Maxillofac Surg, pii: S2468-7855(19)30297-6. doi: 10.1016/j.jormas.2019.12.011. [Epub ahead of print]

- Chenebault C, Diaz-Santos E, Kammerscheit X, Görgen S, Ilioaia C, Streckaite S, Gall A, Robert B, Marcon E, Buisson DA, Benzerara K, Sassi JF, Cassier-Chauvat C, Chauvat F. (2020) A Genetic Toolbox for the New Model Cyanobacterium Cyanothece PCC 7425: A Case Study for the Photosynthetic Production of Limonen. Front Microbiol, 11:586601.doi: 10.3389/fmicb.2020.586601.eCollection 2020.

- Cornilleau C, Chastanet A, Billaudeau C, Carballido-López R. (2020) Methods for Studying Membrane-Associated Bacterial Cytoskeleton Proteins In Vivo by TIRF Microscopy. Methods Mol Biol, 2101:123-133. doi: 10.1007/978-1-0716-0219-5_8.

- David GM, Moreira D, Reboul G, Annenkova NV, Galindo LJ, Bertolino P, López-Archilla AI, Jardillier L, López-García P. (2020) Environmental drivers of plankton protist communities along latitudinal and vertical gradients in the oldest and deepest freshwater lake. Environ Microbiol, doi: 10.1111/1462-2920.15346. Online ahead of print.

- Della-Negra O, Chaussonnerie S, Fonknechten N, Barbance A, Muselet D, Martin DE, Fouteau S, Fischer C, Saaidi PL, Le Paslier D. (2020) Transformation of the recalcitrant pesticide chlordecone by Desulfovibrio sp.86 with a switch from ring-opening dechlorination to reductive sulfidation activity. Sci Rep, 10(1):13545. doi: 10.1038/s41598-020-70124-9.

- Devilliers M., Garrido D., Poidevin M., Rubin T., Le Rouzic A., Montagne J. (2020). Differential Metabolic Sensitivity of Insulin-like-response- and mTORC1-Dependent Overgrowth in Drosophila Fat Cells. bioRxiv .

- Dian C, Pérez-Dorado I, Rivière F, Asensio T, Legrand P, Ritzefeld M, Shen M, Cota E, Meinnel T, Tate EW, Giglione C. (2020) High-resolution snapshots of human N-myristoyltransferase in action illuminate a mechanism promoting N-terminal Lys and Gly myristoylation. Nat Commun, 11(1):1132. doi: 10.1038/s41467-020-14847-3.

- Dossin F, Pinheiro I, Żylicz JJ, Roensch J, Collombet S, Le Saux A, Chelmicki T, Attia M, Kapoor V, Zhan Y, Dingli F, Loew D, Mercher T, Dekker J, Heard E. (2020) SPEN integrates transcriptional and epigenetic control of X-inactivation. Nature, 578(7795):455-460. doi: 10.1038/s41586-020-1974-9. Epub 2020 Feb 5.

- Fontanilla P, Willaume S, Thézé B, Moussa A, Pennarun G, Bertrand P. (2020) Aging: A matter of DNA damage, nuclear envelope alterationsnflammation? Med Sci (Paris), 36(12):1118-1128. doi: 10.1051/medsci/2020241. Epub 2020 Dec 9.

- Frouin A, Dandine-Roulland C, Pierre-Jean M, Jean-François Deleuze JF, Ambroise C, Le Floch E (2020) Exploring the Link Between Additive Heritability and Prediction Accuracy From a Ridge Regression Perspective. Front Genet, 11:581594. doi: 10.3389/fgene.2020.581594. eCollection 2020.> .

- Galupa R, Nora EP, Worsley-Hunt R, Picard C, Gard C, van Bemmel JG, Servant N, Zhan Y, El Marjou F, Johanneau C, Diabangouaya P, Le Saux A, Lameiras S, Pipoli da Fonseca J, Loos F, Gribnau J, Baulande S, Ohler U, Giorgetti L, Heard E. (2020) A Conserved Noncoding Locus Regulates Random Monoallelic Xist Expression across a Topological Boundary. Mol Cell, 77(2):352-367.e8. doi: 10.1016/j.molcel.2019.10.030. Epub 2019 Nov 20.

- Gautreau G, Bazin A, Gachet M, Planel R, Burlot L, Dubois M, Perrin A, Médigue C, Calteau A, Cruveiller S, Matias C, Ambroise C, Rocha EPC, Vallenet D. (2020)  PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph. PLoS Comput Biol, 16(3):e1007732. doi: 10.1371/journal.pcbi.1007732. [Epub ahead of print]

- Giménez-Andrés M, Emeršič T, Antoine-Bally S, Antonny B, Derganc J, Čopič A (2020) Exceptional stability of a perilipin on lipid droplets depends on its polar residues, suggesting multimeric assembly. BioRxiv, doi:

- Gogendeau D, Lemullois M, Le Borgne P, Castelli M, Aubusson-Fleury A, Arnaiz O, Cohen J, Vesque C, Schneider-Maunoury S, Bouhouche K, Koll F, Tassin AM. (2020) MKS-NPHP module proteins control ciliary shedding at the transition zone. PLoS Biol, 18(3):e3000640. doi: 10.1371/journal.pbio.3000640. eCollection 2020 Mar.

- Grassin-Delyle S, Abrial C, Salvator H, Brollo M, Naline E, Devillier P. (2020) The Role of Toll-Like Receptors in the Production of Cytokines by Human Lung Macrophages. J Innate Immun, 12(1):63-73. doi: 10.1159/000494463. Epub 2018 Dec 17.

- Han Z, Jasnovidova O, Haidara N, Tudek A, Kubicek K, Libri D, Stefl R, Porrua O. (2020) Termination of non-coding transcription in yeast relies on both an RNA Pol II CTD interaction domain and a CTD-mimicking region in Sen1. EMBO J, 39(7): e101548. doi: 10.15252/embj.2019101548.

- Hazra D, Andrić V, Palancade B, Rougemaille M, Graille M. (2020) Formation of S. pombe Erh1 homodimer mediates gametogenic gene silencing and meiosis progression. Sci Rep, 10(1):1034. doi: 10.1038/s41598-020-57872-4.

- Ithurbide S, Coste G, Lisboa J, Eugénie N, Bentchikou E, Bouthier de la Tour C, Liger D, Confalonieri F, Sommer S, Quevillon-Cheruel S, Servant P (2020) Natural Transformation in Deinococcus radiodurans: A Genetic Analysis Reveals the Major Roles of DprA, DdrB, RecA, RecF, and RecO Proteins. Front Microbiol, 11:1253. doi: 10.3389/fmicb.2020.01253. eCollection 2020.

- Jeverica S, El Sayed F, Čamernik P, Kocjančič B, Sluga B, Rottman M, Papst L. (2020) Growth detection of Cutibacterium acnes from orthopaedic implant-associated infections in anaerobic bottles from BACTEC and BacT/ALERT blood culture systems and comparison with conventional culture media. Anaerobe, 61:102133. doi: 10.1016/j.anaerobe.2019.102133. Epub 2019 Dec 3.

- Kammerscheit X, Hecker A., Rouhier N., Chauvat F, Cassier-Chauvat C. (2020) Methylglyoxal-detoxification revisited: role of a glutathione transferase in the model cyanobacterium Synechocystis sp. strain PCC 6803. mBio, doi: 10.1128/mBio.00882-20.

- Klotoe BJ, Kurepina N, Zholdibayeva E, Panaiotov S, Kreiswirth BN, Anthony R, Sola C, Refrégier G. (2020) NTF-RINT, a new method for the epidemiological surveillance of MDR Mycobacterium tuberculosis L2/Beijing strains.Tuberculosis (Edinb), 120:101894. doi: 10.1016/ Epub 2019 Dec 9.

- Kyrgyzov O,  Prost V,  Gazut S,  Farcy B,  Brüls T (2020) Binning unassembled short reads based on k-mer abundance covariance using sparse coding. Gigascience, 9(4):giaa028.doi: 10.1093/gigascience/giaa028.

- Laborde-Casterot H, Larabi IA, Dufayet L, Etting I, Alvarez JC, Vodovar D. (2020) Does cannabidiol induce cannabinoid hyperemesis syndrome? Clin Toxicol (Phila), 12:1-2. doi: 10.1080/15563650.2020.1736298. [Epub ahead of print]

- Lamy E, Fall F, Boigne L, Gromov K, Fabresse N, Grassin-Delyle S. (2020) Validation according to European and American regulatory agencies guidelines of an LC-MS/MS method for the quantification of free and total ropivacaine in human plasma. Clin Chem Lab Med, 58(5):701-708. doi: 10.1515/cclm-2018-1298.

- Larabi IA, Martin M, Etting I, Pfau G, Edel Y, Alvarez JC. (2020) Development and validation of liquid chromatography-tandem mass spectrometry targeted screening of 16 fentanyl analogs and U-47700 in hair: Application to 137 authentic samples. Drug Test Anal.. doi: 10.1002/dta.2868. Online ahead of print.

- Laso-Jadart R, Ambroise C, Peterlongo P, Madoui MA. (2020) metaVaR: Introducing metavariant species models for reference-free metagenomic-based population genomics. PLoS One, 15(12):e0244637. doi: 10.1371/journal.pone.0244637. eCollection 2020.

- Laso-Jadart R, Sugier K, Petit E, Labadie K, Peterlongo P, Ambroise C, Wincker P, Jamet JL, Madoui MA. (2020) Investigating population-scale allelic differential expression in wild populations of Oithona similis (Cyclopoida, Claus, 1866). Ecol Evo, 10(16):8894-8905. doi: 10.1002/ece3.6588. eCollection 2020 Aug.

- Lavalou P, Eckert H, Damy L, Constanty F, Majello S, Bitetti A, Graindorge A, Shkumatava A. (2020) Strategies for genetic inactivation of long noncoding RNAs in zebrafish. RNA. 2019 Aug;25(8):897-904. doi: 10.1261/rna.069484.118. Epub 2019 May 1. Erratum in: RNA. 26(4):529.

- Leboutet R, Chen Y, Legouis R, Culetto E (2020) Mitophagy during development and stress in C. elegans. Mech Ageing Dev, 189:111266. doi: 10.1016/j.mad.2020.111266. Epub 2020 May 23.

- Leconte J, Benites LF, Vannier T, Wincker P, Piganeau G, Jaillon O. (2019) Genome Resolved Biogeography of Mamiellales. Genes (Basel), 11(1). pii: E66. doi: 10.3390/genes11010066.

- Liu W, Boudry P, Bohn C, Bouloc P. (2020) Staphylococcus aureus pigmentation is not controlled by Hfq. BMC Res Notes,13(1):63. doi: 10.1186/s13104-020-4934-4.

- Loiseau V, Herniou EA, Moreau Y, Lévêque N, Meignin C, Daeffler L, Federici B, Cordaux R, Gilbert C. (2020) Wide spectrum and high frequency of genomic structural variation, including transposable elements, in large double-stranded DNA viruses. Virus Evol, 6(1):vez060. doi: 10.1093/ve/vez060. eCollection 2020 Jan.

- Loiseau V, Cordaux R, Giraud I, Beby-Defaux A, Lévêque N, Gilbert C. (2020) Characterization of a new case of XMLV (Bxv1) contamination in the human cell line Hep2 (clone 2B). Sci Rep.10(1):16046. doi: 10.1038/s41598-020-73169-y.

- Luo Y, Xiang S, Hooikaas PJ, van Bezouwen L, Jijumon AS, Janke C, Förster F, Akhmanova A, Baldus M. (2020) Direct observation of dynamic protein interactions involving human microtubules using solid-state NMR spectroscopy. Nat Commun, 11(1):18. doi: 10.1038/s41467-019-13876-x.

- Malbert B, Burger M, Lopez-Obando M, Baudry K, Launay-Avon A, Härtel B, Verbitskiy D, Jörg A, Berthomé R, Lurin C, Takenaka M, Delannoy E. (2020) The Analysis of the Editing Defects in the dyw2 Mutant -Provides New Clues for the Prediction of RNA Targets of Arabidopsis E+-Class PPR Proteins. Plants (Basel), 9(2). doi: 10.3390/plants9020280.

- Maroc L, Zhou-Li Y, Boisnard S, Fairhead C. (2020) A single Ho-induced double-strand break at the MAT locus is lethal in Candida glabrata. PLoS Genet, 16(10):e1008627. doi: 10.1371/journal.pgen.1008627. eCollection 2020 Oct.

- Massacci FR, Tofani S, Forte C, Bertocchi M, Lovito C, Orsini S, Tentellini M, Marchi L, Lemonnier G, Luise D, Blanc F, Castinel A, Bevilacqua C, Rogel-Gaillard C, Pezzotti G, Estellé J, Trevisi P, Magistrali CF. (2020)  Host genotype and amoxicillin administration affect the incidence of diarrhoea and faecal microbiota of weaned piglets during a natural multiresistant ETEC infection. J Anim Breed Genet, 137(1):60-72. doi: 10.1111/jbg.12432. Epub 2019 Sep 3.

- Méar L, Herr M, Fauconnier A, Pineau C, Vialard F. (2020) Polymorphisms and endometriosis: a systematic review and meta-analyses. Hum Reprod Update, 26(1):73-102. doi: 10.1093/humupd/dmz034.

- Molinari CA, Palacin F, Poinsard L, Billat VL (2020) Determination of Submaximal and Maximal Training Zones From a 3-Stage, Variable-Duration, Perceptually Regulated Track Test. Int J Sports Physiol Perform, 15:1-9. doi: 10.1123/ijspp.2019-0423. [Epub ahead of print]

- Oppezzo A, Bourseguin J, Renaud E, Pawlikowska P, Rosselli F. (2020) Microphthalmia transcription factor expression contributes to bone marrow failure in Fanconi anemia.J Clin Invest, 130(3):1377-1391. doi: 10.1172/JCI131540.

- Randazzo P, Anba-Mondoloni J, Aubert-Frambourg A, Guillot A, Pechoux C, Vidic J, Auger S. (2020) Bacillus subtilis Regulators MntR and Zur Participate in Redox Cycling, Antibiotic Sensitivity, and Cell Wall Plasticity. J Bacteriol, 202(5). pii: e00547-19. doi: 10.1128/JB.00547-19. Print 2020 Feb 11

- Reñé A, Auladell A, Reboul G, Moreira D, López-García P. (2020) Performance of the melting seawater-ice elution method on the metabarcoding characterization of benthic protist communities. Environ Microbiol Rep, 12(3):314-323. doi: 10.1111/1758-2229.12834.

- Sabeti Azad M, Okuda M, Cyrenne M, Bourge M, Heck MP, Yoshizawa S, Fourmy D. (2020) Fluorescent aminoglycoside antibiotics and methods for accurately monitoring uptake by bacteria. ACS Infect Dis, doi: 10.1021/acsinfecdis.9b00421. [Epub ahead of print]

- Saghaï A, Zivanovic Y, Moreira D, Tavera R, López-García P. (2020) A Novel Microbialite-Associated Phototrophic Chloroflexi Lineage Exhibiting a Quasi-Clonal Pattern along Depth.Genome Biol Evo, 12(7):1207-1216. doi: 10.1093/gbe/evaa122.

- Salvator H, Grassin-Delyle S, Naline E, Brollo M, Fournier C, Couderc LJ, Devillier P. (2020) Contrasting Effects of Adipokines on the Cytokine Production by Primary Human Bronchial Epithelial Cells: Inhibitory Effects of Adiponectin. Front Pharmacol, 11:56. doi: 10.3389/fphar.2020.00056. eCollection 2020

- Sena E, Bou-Rouphael J, Rocques N, Carron-Homo C, Durand BC. (2020) Mcl1 protein levels and Caspase-7 executioner protease control axial organizer cells survival. Dev Dyn, doi: 10.1002/dvdy.169. [Epub ahead of print]

- Song Z, Hu Y, Iorga BI, Vallières C, Fisher N, Meunier B. (2020) Mutational analysis of the Qi-site proton pathway in yeast cytochrome bc1 complex. Biochem Biophys Res Commun, 523(3):615-619. doi: 10.1016/j.bbrc.2019.12.102. Epub 2020 Jan 12.

- Steunou AS, Babot M, Bourbon ML, Tambosi R, Durand A, Liotenberg S, Krieger-Liszkay A, Yamaichi Y, Ouchane S. (2020) Additive effects of metal excess and superoxide, a highly toxic mixture in bacteria. Microb Biotechnol, 13(5):1515-1529. doi: 10.1111/1751-7915.13589. Epub 2020 Jun 19.

- Steunou AS, Durand A, Bourbon ML, Babot M, Tambosi R, Liotenberg S, Ouchane S. (2020) Cadmium and Copper Cross-Tolerance. Cu+ Alleviates Cd2 + Toxicity, and Both Cations Target Heme and Chlorophyll Biosynthesis Pathway in Rubrivivax gelatinosus. Front Microbiol, 11:893. doi: 10.3389/fmicb.2020.00893. eCollection 2020.

- Vaillant G, Martin M, Groos E, Larabi IA, Alvarez JC, Arnulf I.A strange New Year's Eve: triggers in Kleine-Levin syndrome. J Clin Sleep Med. 2020 Oct 7. doi: 10.5664/jcsm.8858. Online ahead of print.

- Vallenet D, Calteau A, Dubois M, Amours P, Bazin A, Beuvin M, Burlot L, Bussell X, Fouteau S, Gautreau G, Lajus A, Langlois J, Planel R, Roche D, Rollin J, Rouy Z, Sabatet V, Médigue C. (2020) MicroScope: an integrated platform for the annotation and exploration of microbial gene functions through genomic, pangenomic and metabolic comparative analysis. Nucleic Acids Res, 48(D1):D579-D589. doi: 10.1093/nar/gkz926.

- Vaubourg C, Gicquel E, Richard I, Lostal W et Bellec J (2020) Minimal Consequences of CMAH and DBA/2J Background on a FKRP Deficient Model. J Neuromuscul Dis. doi: 10.3233/JND-200487. Online ahead of print.

- Veaudor T, Blanc-Garin V, Chenebault C, Diaz-Santos E, Sassi JF, Cassier-Chauvat C, Chauvat F. (2020) Recent Advances in the Photoautotrophic Metabolism of Cyanobacteria: Biotechnological Implications. Life (Basel), 10(5):71. doi: 10.3390/life10050071.

- Veyssière M, Perea J, Michou L, Boland A, Caloustian C, Olaso R, Deleuze JF,Cornelis F, Petit-Teixeira E, Chaudru V. (2019) A novel nonsense variant in SUPT20H gene associated with Rheumatoid Arthritis identified by Whole Exome Sequencing of multiplex families. PLoS ONE 14(3): e0213387.

- Vigouroux C., Henriot V., Le Clainche C. (2020) Talin dissociates from RIAM and associates to vinculin sequentially in response to the actomyosin force. Nat Comm,

- Wang Y, Osman JR, DuBow MS. (2020) Bacterial Communities on the Surface of the Mineral Sandy Soil from the Desert of Maine (USA). Curr Microbiol, doi: 10.1007/s00284-020-01946-z. [Epub ahead of print]

- Yousuf M, Iuliani I, Veetil RT, Seshasayee ASN, Sclavi B, Cosentino Lagomarsino M. (2020) Early fate of exogenous promoters in E. coli. Nucleic Acids Res, 48(5):2348-2356. doi: 10.1093/nar/gkz1196.

- Yubuki N, Galindo LJ, Reboul G, López-García P, Brown MW, Pollet N, Moreira D. (2020) Ancient Adaptive Lateral Gene Transfers in the Symbiotic Opalina-Blastocystis Stramenopile Lineage. Mol Biol Evol, 37(3):651-659. doi: 10.1093/molbev/msz250.